Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples
Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma has been widely adopted. Recently, NIPT coverage has expanded to detect subchromosomal abnormalities including the 22q11.2 deletion. Validation of a SNP-based NIPT for detection of 22q11.2 deletions demonstrat...
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| creator | Ravi, Harini McNeill, Gabriel Goel, Shruti Meltzer, Steven D Hunkapiller, Nathan Ryan, Allison Levy, Brynn Demko, Zachary P |
| description | Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma has been widely adopted. Recently, NIPT coverage has expanded to detect subchromosomal abnormalities including the 22q11.2 deletion. Validation of a SNP-based NIPT for detection of 22q11.2 deletions demonstrating a high sensitivity (97.8%) and specificity (99.75%) has been reported. We sought to further demonstrate the performance of a revised version of the test in a larger set of pregnancy plasma samples.
Blood samples from pregnant women (10 with 22q11.2-deletion‒affected fetuses and 390 negative controls) were successfully analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. The sensitivity and specificity of the assay were measured.
Sensitivity of the assay was 90% (9/10), and specificity of the assay was 99.74% (389/390), with a corresponding false positive-rate of 0.26%.
The data presented in this study add to the growing body of evidence demonstrating the ability of the SNP-based NIPT to detect 22q11.2 deletions with high sensitivity and specificity. |
| doi_str_mv | 10.1371/journal.pone.0193476 |
| format | Article |
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Blood samples from pregnant women (10 with 22q11.2-deletion‒affected fetuses and 390 negative controls) were successfully analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. The sensitivity and specificity of the assay were measured.
Sensitivity of the assay was 90% (9/10), and specificity of the assay was 99.74% (389/390), with a corresponding false positive-rate of 0.26%.
The data presented in this study add to the growing body of evidence demonstrating the ability of the SNP-based NIPT to detect 22q11.2 deletions with high sensitivity and specificity.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0193476</identifier><identifier>PMID: 29474437</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abnormalities ; Adult ; Amniocentesis ; Analysis ; Aneuploidy ; Assaying ; Biology and Life Sciences ; Children & youth ; Chromosome Deletion ; Chromosomes ; Chromosomes, Human, Pair 22 ; Clonal deletion ; Congenital diseases ; Deoxyribonucleic acid ; DNA ; Female ; Fetuses ; Gene deletion ; Genetic aspects ; Genetic Testing - methods ; Gynecology ; Humans ; Intermetallic compounds ; Laboratories ; Medicine and Health Sciences ; Mothers ; Nickel base alloys ; Nickel compounds ; Obstetrics ; Physiological aspects ; Plasma - metabolism ; Platinum compounds ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal diagnosis ; Prenatal Diagnosis - methods ; Research and Analysis Methods ; Sampling methods ; Sensitivity ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Women</subject><ispartof>PloS one, 2018-02, Vol.13 (2), p.e0193476-e0193476</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Ravi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Ravi et al 2018 Ravi et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-bea2a7cfadc321ee365b63aa9aaca504f117f7b15db664323fc5a617ceafba0d3</citedby><cites>FETCH-LOGICAL-c692t-bea2a7cfadc321ee365b63aa9aaca504f117f7b15db664323fc5a617ceafba0d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825123/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825123/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23864,27922,27923,53789,53791,79370,79371</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29474437$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Chan, Kelvin Yuen Kwong</contributor><creatorcontrib>Ravi, Harini</creatorcontrib><creatorcontrib>McNeill, Gabriel</creatorcontrib><creatorcontrib>Goel, Shruti</creatorcontrib><creatorcontrib>Meltzer, Steven D</creatorcontrib><creatorcontrib>Hunkapiller, Nathan</creatorcontrib><creatorcontrib>Ryan, Allison</creatorcontrib><creatorcontrib>Levy, Brynn</creatorcontrib><creatorcontrib>Demko, Zachary P</creatorcontrib><title>Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma has been widely adopted. Recently, NIPT coverage has expanded to detect subchromosomal abnormalities including the 22q11.2 deletion. Validation of a SNP-based NIPT for detection of 22q11.2 deletions demonstrating a high sensitivity (97.8%) and specificity (99.75%) has been reported. We sought to further demonstrate the performance of a revised version of the test in a larger set of pregnancy plasma samples.
Blood samples from pregnant women (10 with 22q11.2-deletion‒affected fetuses and 390 negative controls) were successfully analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. The sensitivity and specificity of the assay were measured.
Sensitivity of the assay was 90% (9/10), and specificity of the assay was 99.74% (389/390), with a corresponding false positive-rate of 0.26%.
The data presented in this study add to the growing body of evidence demonstrating the ability of the SNP-based NIPT to detect 22q11.2 deletions with high sensitivity and specificity.</description><subject>Abnormalities</subject><subject>Adult</subject><subject>Amniocentesis</subject><subject>Analysis</subject><subject>Aneuploidy</subject><subject>Assaying</subject><subject>Biology and Life Sciences</subject><subject>Children & youth</subject><subject>Chromosome Deletion</subject><subject>Chromosomes</subject><subject>Chromosomes, Human, Pair 22</subject><subject>Clonal deletion</subject><subject>Congenital diseases</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Female</subject><subject>Fetuses</subject><subject>Gene deletion</subject><subject>Genetic aspects</subject><subject>Genetic Testing - methods</subject><subject>Gynecology</subject><subject>Humans</subject><subject>Intermetallic compounds</subject><subject>Laboratories</subject><subject>Medicine and Health Sciences</subject><subject>Mothers</subject><subject>Nickel base alloys</subject><subject>Nickel compounds</subject><subject>Obstetrics</subject><subject>Physiological aspects</subject><subject>Plasma - metabolism</subject><subject>Platinum compounds</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Pregnancy</subject><subject>Prenatal diagnosis</subject><subject>Prenatal Diagnosis - methods</subject><subject>Research and Analysis Methods</subject><subject>Sampling methods</subject><subject>Sensitivity</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Women</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9-L1DAQx4so3nn6H4gWBNGHrk3SJtsX4Tj8sXB44um9hmk63c2SNr0mXfS_N93tHVu5B-lDhsxnvjOZzkTRS5IuCBPkw9YOfQtm0dkWFykpWCb4o-g0GDThNGWPj-yT6Jlz2zTN2ZLzp9EJLTKRZUycRv4GjK7Aa9vGto4hvv72PSnBYRW3tk10uwOndxh3PbbgwcQenY-9jSv0qIK1wbjG0UHpLSELGhwG93K6jRvwOBYZdwZcA7GDpjPonkdPajAOX0znWfTr86efF1-Ty6svq4vzy0TxgvqkRKAgVA2VYpQgMp6XnAEUAAryNKsJEbUoSV6VnGeMslrlwIlQCHUJacXOotcH3c5YJ6eGOUnTVPCCMEoDsToQlYWt7HrdQP9HWtByf2H7tYTea2VQBnyZqbwQBaUZ5aKkoT6yLNKiFoqnGLQ-TtmGssFKYet7MDPRuafVG7m2O5kvaU4oCwLvJoHe3g6hz7LRTqEx0KIdDnUXS8HIWPebf9CHXzdRawgP0G1tQ141isrznIZRYHyfdvEAFb4KG63CdNU63M8C3s8CAuPxt1_D4JxcXf_4f_bqZs6-PWI3CMZvnDXDOE1uDmYHUPXWuR7r-yaTVI7LcdcNOS6HnJYjhL06_kH3QXfbwP4C_5gJfQ</recordid><startdate>20180223</startdate><enddate>20180223</enddate><creator>Ravi, Harini</creator><creator>McNeill, Gabriel</creator><creator>Goel, Shruti</creator><creator>Meltzer, Steven D</creator><creator>Hunkapiller, Nathan</creator><creator>Ryan, Allison</creator><creator>Levy, Brynn</creator><creator>Demko, Zachary P</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20180223</creationdate><title>Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples</title><author>Ravi, Harini ; McNeill, Gabriel ; Goel, Shruti ; Meltzer, Steven D ; Hunkapiller, Nathan ; Ryan, Allison ; Levy, Brynn ; Demko, Zachary P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-bea2a7cfadc321ee365b63aa9aaca504f117f7b15db664323fc5a617ceafba0d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Abnormalities</topic><topic>Adult</topic><topic>Amniocentesis</topic><topic>Analysis</topic><topic>Aneuploidy</topic><topic>Assaying</topic><topic>Biology and Life Sciences</topic><topic>Children & youth</topic><topic>Chromosome Deletion</topic><topic>Chromosomes</topic><topic>Chromosomes, Human, Pair 22</topic><topic>Clonal deletion</topic><topic>Congenital diseases</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Female</topic><topic>Fetuses</topic><topic>Gene deletion</topic><topic>Genetic aspects</topic><topic>Genetic Testing - methods</topic><topic>Gynecology</topic><topic>Humans</topic><topic>Intermetallic compounds</topic><topic>Laboratories</topic><topic>Medicine and Health Sciences</topic><topic>Mothers</topic><topic>Nickel base alloys</topic><topic>Nickel compounds</topic><topic>Obstetrics</topic><topic>Physiological aspects</topic><topic>Plasma - metabolism</topic><topic>Platinum compounds</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Pregnancy</topic><topic>Prenatal diagnosis</topic><topic>Prenatal Diagnosis - methods</topic><topic>Research and Analysis Methods</topic><topic>Sampling methods</topic><topic>Sensitivity</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Women</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ravi, Harini</creatorcontrib><creatorcontrib>McNeill, Gabriel</creatorcontrib><creatorcontrib>Goel, Shruti</creatorcontrib><creatorcontrib>Meltzer, Steven D</creatorcontrib><creatorcontrib>Hunkapiller, Nathan</creatorcontrib><creatorcontrib>Ryan, Allison</creatorcontrib><creatorcontrib>Levy, Brynn</creatorcontrib><creatorcontrib>Demko, Zachary P</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ravi, Harini</au><au>McNeill, Gabriel</au><au>Goel, Shruti</au><au>Meltzer, Steven D</au><au>Hunkapiller, Nathan</au><au>Ryan, Allison</au><au>Levy, Brynn</au><au>Demko, Zachary P</au><au>Chan, Kelvin Yuen Kwong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-02-23</date><risdate>2018</risdate><volume>13</volume><issue>2</issue><spage>e0193476</spage><epage>e0193476</epage><pages>e0193476-e0193476</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma has been widely adopted. Recently, NIPT coverage has expanded to detect subchromosomal abnormalities including the 22q11.2 deletion. Validation of a SNP-based NIPT for detection of 22q11.2 deletions demonstrating a high sensitivity (97.8%) and specificity (99.75%) has been reported. We sought to further demonstrate the performance of a revised version of the test in a larger set of pregnancy plasma samples.
Blood samples from pregnant women (10 with 22q11.2-deletion‒affected fetuses and 390 negative controls) were successfully analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. The sensitivity and specificity of the assay were measured.
Sensitivity of the assay was 90% (9/10), and specificity of the assay was 99.74% (389/390), with a corresponding false positive-rate of 0.26%.
The data presented in this study add to the growing body of evidence demonstrating the ability of the SNP-based NIPT to detect 22q11.2 deletions with high sensitivity and specificity.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29474437</pmid><doi>10.1371/journal.pone.0193476</doi><tpages>e0193476</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abnormalities Adult Amniocentesis Analysis Aneuploidy Assaying Biology and Life Sciences Children & youth Chromosome Deletion Chromosomes Chromosomes, Human, Pair 22 Clonal deletion Congenital diseases Deoxyribonucleic acid DNA Female Fetuses Gene deletion Genetic aspects Genetic Testing - methods Gynecology Humans Intermetallic compounds Laboratories Medicine and Health Sciences Mothers Nickel base alloys Nickel compounds Obstetrics Physiological aspects Plasma - metabolism Platinum compounds Polymorphism, Single Nucleotide Pregnancy Prenatal diagnosis Prenatal Diagnosis - methods Research and Analysis Methods Sampling methods Sensitivity Single nucleotide polymorphisms Single-nucleotide polymorphism Women |
| title | Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples |
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